During the Spanish colonial period in the Philippines, merchants travelling in and out of Laguna de Bay via Napindan had issues with the formation of sandbars that blocked or clogged the waterway.

[5]: 180  According to a legend, based on the barangay's profile on the official website of Taguig, the son of a datu from Tipas arrived at the area, which at that time was an island due to surrounding creeks and rivers, and was abducted by bandits.

[8] On the eve of May 9, 1896, a meeting consisting of Andrés Bonifacio, Emilio Aguinaldo, Pío Valenzuela, and several high-ranking commanders of the Katipunan took place in a lighthouse located at the barrio, where they listened to Valenzuela's report of his visit to José Rizal, who was exiled in Dapitan, regarding Rizal's advise about their planned revolution against the Spaniards.

[9] Following the country's independence from Spain on June 12, 1898, Napindan was placed under Pedro Esguerra as the village president (Filipino: pangulo ng nayon).

[5]: 30 During the Battle of Taguig on March 19, 1899, as part of the Philippine-American War, USS Laguna de Bay of the United States Asiatic Squadron destroyed the lighthouse to deprive the Katipunan command and control over the area.